Function_ComputePairWiseModelDistances_OU: Function_ComputePairWiseModelDistances_OU: function to...

In radamsRHA/PRDATR: Computing probabilistic distances between phylogenetic models of continuous trait evolution

Description

This function returns a list of pairwise distances under the OU models

Usage

Function_ComputePairWiseModelDistances_OU(
  phylogeny.TreeSet,
  matrix.ModelParams
)

Arguments

phylogeny.TreeSet	Set of phylogenetic trees
matrix.ModelParams	Matrix of model parameters (OU) for each tree in the given set

Value

List List of pairwise model distances

Examples

################
# Load depends #
################
library(ape)
library(geiger)
library(gaussDiff)

#########################
# Simulate random trees #
#########################
handle.SimulatedRandomTree <- rmtree(N = 1, n = 10)
handle.SimulatedRandomTrees <- list()
class(handle.SimulatedRandomTrees) <- "multiPhylo"
handle.SimulatedRandomTrees[[1]] <- handle.SimulatedRandomTrees[[2]] <- handle.SimulatedRandomTrees[[3]] <- handle.SimulatedRandomTrees[[4]] <- handle.SimulatedRandomTrees[[5]] <- handle.SimulatedRandomTree[[1]]
vector.SimulatedDataset <- fastBM(tree = handle.SimulatedRandomTrees[[1]], a = 0, sig2 = 1, alpha = 2)

#######################
# Fit models to trees #
#######################
handle.FittedPhylogeneticModels <- Function_FitCont_TreeSet_0U(phylogeny.TreeSet = handle.SimulatedRandomTrees, vector.InputData = vector.SimulatedDataset)

##############################
# Compute pairwise distances #
##############################
handle.Results <- Function_ComputePairWiseModelDistances_OU(phylogeny.TreeSet = handle.SimulatedRandomTrees, matrix.ModelParams = handle.FittedPhylogeneticModels)

radamsRHA/PRDATR documentation built on Dec. 25, 2021, 11:44 a.m.